BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy7583
(451 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|N Chain N, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1210
Score = 541 bits (1395), Expect = e-154, Method: Compositional matrix adjust.
Identities = 270/484 (55%), Positives = 335/484 (69%), Gaps = 82/484 (16%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
MGVY+TN+ VRMDT+A++LYYP KPL TTR
Sbjct: 767 MGVYLTNYQVRMDTMANILYYPQKPLATTR------------------------------ 796
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
SMEYL+FRELPAG N+IVAILCY+GYNQEDS+I+N ++++RG FR
Sbjct: 797 ---------------SMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFR 841
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
S+F+R+Y D E K E+FE+P R T M++ YDKL+DDG+IAPG RVSG+D++I
Sbjct: 842 SIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIII 901
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GKT +P + +EL T+ +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS R
Sbjct: 902 GKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTR 961
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
IPQIGDKFASRHGQKGT G+ YR E
Sbjct: 962 IPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLS 1021
Query: 266 -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
VS+ G GDATPF D V V+ +S LL+ +G+Q RG EVM++GHTGRK+ AQVFLGPTY
Sbjct: 1022 KVSALSGFEGDATPFTD-VTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTY 1080
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQRLKH+VDDKIH+RARGPVQIL RQP+EGR+RDGGLRFGEMERDCQISHG + LRERL
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140
Query: 385 FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
F+ SD YR+ VC+ CGLIAIA+ + +++EC+ C+N+T+ SQV LPYAAKLLFQELMSMNI
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200
Query: 445 APRL 448
APRL
Sbjct: 1201 APRL 1204
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|B Chain B, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|B Chain B, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|B Chain B, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|B Chain B, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|B Chain B, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|B Chain B, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|B Chain B, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
pdb|4BBR|B Chain B, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|B Chain B, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1224
Score = 535 bits (1379), Expect = e-152, Method: Compositional matrix adjust.
Identities = 266/485 (54%), Positives = 328/485 (67%), Gaps = 83/485 (17%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
MGV++TN++VRMDT+A++LYYP KPL TTR
Sbjct: 778 MGVFLTNYNVRMDTMANILYYPQKPLGTTR------------------------------ 807
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
+MEYL+FRELPAG N+IVAI CY+GYNQEDS+I+N S+++RG FR
Sbjct: 808 ---------------AMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFR 852
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
S+FFRSY D E K E FEKP R M++ YDKLDDDG+IAPG+RVSG+DV+I
Sbjct: 853 SLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVII 912
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GKT + +E+EL T SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +
Sbjct: 913 GKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTK 972
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQE----------------------------------- 265
IPQIGDKFASRHGQKGT GI YR+E
Sbjct: 973 IPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLS 1032
Query: 266 -VSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
V++ G GDA+PF D + V+ IS LL+E+GYQ RG EVM+NGHTG+K+ AQ+F GPTY
Sbjct: 1033 KVAALSGNEGDASPFTD-ITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTY 1091
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQRL+HMVDDKIH+RARGP+Q+L RQP+EGR+RDGGLRFGEMERDC I+HGAA FL+ERL
Sbjct: 1092 YQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERL 1151
Query: 385 FEVSDPYRIHVCNFCGLIA-IANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMN 443
E SD +R+H+C CGL+ IA + +N FECKGC NK I Q+ +PYAAKLLFQELM+MN
Sbjct: 1152 MEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMN 1211
Query: 444 IAPRL 448
I PRL
Sbjct: 1212 ITPRL 1216
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 342 bits (877), Expect = 2e-94, Method: Compositional matrix adjust.
Identities = 192/486 (39%), Positives = 266/486 (54%), Gaps = 83/486 (17%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+Y N+ +R DT AH+L+YP +PLV TR+++ I+ YT
Sbjct: 680 LGLYAANYQLRTDTRAHLLHYPQRPLVQTRALD----------------IIGYTNR---- 719
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
PAG N+I+A++ +TGYN EDS+I+N S+VERG +R
Sbjct: 720 -------------------------PAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYR 754
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
S FFR Y E K G QE++ P Y L+D+G+++P + V G DV+I
Sbjct: 755 STFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLI 814
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GK ++ P E + + +KRD S R+ E GIVD V++T +G K K+RVR +R
Sbjct: 815 GK-VSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLR 873
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQ------------------------------------ 264
IP IGDKFASRHGQKG G+ Q
Sbjct: 874 IPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAG 933
Query: 265 EVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
+ ++ G I DATPF ++++ + +YGY EV ++G TG+KI ++++ G Y
Sbjct: 934 KYAALSGNIVDATPFY-KTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVY 992
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQ+L HMV DKIH+RARGPVQIL RQP EGRAR+GGLRFGEMERDC I G A L++RL
Sbjct: 993 YQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRL 1052
Query: 385 FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
+ SD I+VC+ CG I + N + C +K+ + V + YA KLL QELMSM I
Sbjct: 1053 LDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMII 1112
Query: 445 APRLMV 450
+PRL++
Sbjct: 1113 SPRLIL 1118
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 341 bits (875), Expect = 5e-94, Method: Compositional matrix adjust.
Identities = 191/486 (39%), Positives = 266/486 (54%), Gaps = 83/486 (17%)
Query: 1 MGVYITNFHVRMDTLAHVLYYPHKPLVTTRSMEYLRFRELPAGINSIVAILCYTGYNQED 60
+G+Y N+ +R DT AH+L+YP +PLV TR+++ I+ YT
Sbjct: 677 LGLYAANYQLRTDTRAHLLHYPQRPLVQTRALD----------------IIGYTNR---- 716
Query: 61 SVILNASAVERGYFRSMEYLRFRELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFR 120
PAG N+I+A++ +TGYN EDS+I+N S+VERG +R
Sbjct: 717 -------------------------PAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYR 751
Query: 121 SVFFRSYKDAESKRIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVI 180
S FFR Y E K G QE++ P Y L+D+G+++P + V G DV+I
Sbjct: 752 STFFRLYSTEEVKYPGGQEDKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLI 811
Query: 181 GKTITLPENEDELEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVR 240
GK ++ P E + + +KRD S R+ E GIVD V++T +G K K+RVR +R
Sbjct: 812 GK-VSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLR 870
Query: 241 IPQIGDKFASRHGQKGTCGIQYRQ------------------------------------ 264
IP IGDKFASRHGQKG G+ Q
Sbjct: 871 IPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAG 930
Query: 265 EVSSNKGEIGDATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTY 324
+ ++ G I DATPF ++++ + YGY EV+++G TG+KI ++++ G Y
Sbjct: 931 KYAALSGNIVDATPFYKT-PIEQLQNEILRYGYLPDATEVVYDGRTGQKIKSRIYFGVVY 989
Query: 325 YQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERL 384
YQ+L HMV DK+H+RARGPVQIL RQP EGRAR+GGLRFGEMERDC I G A L++RL
Sbjct: 990 YQKLHHMVADKLHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRL 1049
Query: 385 FEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNI 444
+ SD I+VC+ CG I + N + C +K+ + V + YA KLL QELMSM I
Sbjct: 1050 LDNSDRTMIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMII 1109
Query: 445 APRLMV 450
+PRL++
Sbjct: 1110 SPRLVL 1115
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1119
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 46/146 (31%), Positives = 79/146 (54%), Gaps = 16/146 (10%)
Query: 299 LRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARD 358
L+G V+++G TG I + +G + +L HMV+DK+H+R+ GP ++ +QP+ G+A+
Sbjct: 968 LQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQF 1027
Query: 359 GGLRFGEMERDCQISHGAAQFLRERLFEVSDPYRIHVCNFCGLIAIANMRNNTFECKGCK 418
GG RFGEME ++GAA L+E L SD + G RN +E
Sbjct: 1028 GGQRFGEMEVWALEAYGAAHTLQEMLTLKSD-------DIEG-------RNAAYEA--II 1071
Query: 419 NKTQISQVRLPYAAKLLFQELMSMNI 444
+ + +P + ++L +EL ++ +
Sbjct: 1072 KGEDVPEPSVPESFRVLVKELQALAL 1097
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 58/216 (26%), Positives = 99/216 (45%), Gaps = 25/216 (11%)
Query: 85 LPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQFE 143
L G N +VAI+ + GYN ED+++++ ++R ++ S+ Y+ +A ++G + +
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRD 725
Query: 144 KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKR--FS 201
P+ + A LD++G++ G V D+++G+T E+E E R F
Sbjct: 726 IPH------LSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFG 779
Query: 202 K-----RDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV--------RIPQIGDKF 248
+ +D S + E GIV + + D K VR V R Q+GDK
Sbjct: 780 EKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKL 839
Query: 249 ASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVN 284
A+RHG KG E + + D TP + +N
Sbjct: 840 ANRHGNKGVVAKILPVE---DMPHLPDGTPVDVILN 872
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 43/114 (37%), Positives = 64/114 (56%)
Query: 276 ATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDK 335
ATP D +I LL+ G +++G TG + V +G Y +L H+VDDK
Sbjct: 1183 ATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDK 1242
Query: 336 IHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSD 389
+H+R+ G ++ +QP+ G+A+ GG RFGEME ++GAA L+E L SD
Sbjct: 1243 MHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 57/111 (51%), Gaps = 9/111 (8%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQF 142
EL G N VA + + GYN EDS++++ V+ F ++ + + ++G +E
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA 852
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL 193
+ PN + A KLD+ GI+ G V+G D+++GK P+ E +L
Sbjct: 853 DIPN------VGEAALSKLDESGIVYIGAEVTGGDILVGKVT--PKGETQL 895
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|4IGC|C Chain C, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|H Chain H, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1342
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 43/114 (37%), Positives = 64/114 (56%)
Query: 276 ATPFNDAVNVQKISTLLQEYGYQLRGNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDK 335
ATP D +I LL+ G +++G TG + V +G Y +L H+VDDK
Sbjct: 1183 ATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDK 1242
Query: 336 IHSRARGPVQILVRQPMEGRARDGGLRFGEMERDCQISHGAAQFLRERLFEVSD 389
+H+R+ G ++ +QP+ G+A+ GG RFGEME ++GAA L+E L SD
Sbjct: 1243 MHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 57/111 (51%), Gaps = 9/111 (8%)
Query: 84 ELPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQF 142
EL G N VA + + GYN EDS++++ V+ F ++ + + ++G +E
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA 852
Query: 143 EKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL 193
+ PN + A KLD+ GI+ G V+G D+++GK P+ E +L
Sbjct: 853 DIPN------VGEAALSKLDESGIVYIGAEVTGGDILVGKVT--PKGETQL 895
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 56/89 (62%)
Query: 301 GNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGG 360
G V+++G TG + +G + +L HMV+DK+H+R+ GP ++ +QP+ G+A+ GG
Sbjct: 969 GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGG 1028
Query: 361 LRFGEMERDCQISHGAAQFLRERLFEVSD 389
RFGEME ++GAA L+E L SD
Sbjct: 1029 QRFGEMEVWALEAYGAAHTLQEMLTIKSD 1057
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 59/216 (27%), Positives = 97/216 (44%), Gaps = 25/216 (11%)
Query: 85 LPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQFE 143
L G N +VAI+ + GYN ED+++++ ++R ++ S+ Y+ +A ++G + +
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRD 724
Query: 144 KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKR--FS 201
P+ + A LD++GI+ G V D+++G+T E E E R F
Sbjct: 725 IPH------LSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 778
Query: 202 K-----RDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV--------RIPQIGDKF 248
+ +D S + E GIV + D K VR V R Q+GDK
Sbjct: 779 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 838
Query: 249 ASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVN 284
A+RHG KG E + + D TP + +N
Sbjct: 839 ANRHGNKGVVAKILPVE---DMPHLPDGTPVDVILN 871
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase-
Includes Complete Structure With Side-Chains (Except For
Disordered Regions)-Further Refined From Original
Deposition-Contains Additional Sequence Information
Length = 1119
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 56/89 (62%)
Query: 301 GNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGG 360
G V+++G TG + +G + +L HMV+DK+H+R+ GP ++ +QP+ G+A+ GG
Sbjct: 970 GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGG 1029
Query: 361 LRFGEMERDCQISHGAAQFLRERLFEVSD 389
RFGEME ++GAA L+E L SD
Sbjct: 1030 QRFGEMEVWALEAYGAAHTLQEMLTIKSD 1058
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 59/216 (27%), Positives = 97/216 (44%), Gaps = 25/216 (11%)
Query: 85 LPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQFE 143
L G N +VAI+ + GYN ED+++++ ++R ++ S+ Y+ +A ++G + +
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRD 725
Query: 144 KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKR--FS 201
P+ + A LD++GI+ G V D+++G+T E E E R F
Sbjct: 726 IPH------LSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 779
Query: 202 K-----RDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV--------RIPQIGDKF 248
+ +D S + E GIV + D K VR V R Q+GDK
Sbjct: 780 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 839
Query: 249 ASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVN 284
A+RHG KG E + + D TP + +N
Sbjct: 840 ANRHGNKGVVAKILPVE---DMPHLPDGTPVDVILN 872
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For Structural
Studies
Length = 1119
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 56/89 (62%)
Query: 301 GNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGG 360
G V+++G TG + +G + +L HMV+DK+H+R+ GP ++ +QP+ G+A+ GG
Sbjct: 970 GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGG 1029
Query: 361 LRFGEMERDCQISHGAAQFLRERLFEVSD 389
RFGEME ++GAA L+E L SD
Sbjct: 1030 QRFGEMEVWALEAYGAAHTLQEMLTIKSD 1058
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 59/216 (27%), Positives = 97/216 (44%), Gaps = 25/216 (11%)
Query: 85 LPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQFE 143
L G N +VAI+ + GYN ED+++++ ++R ++ S+ Y+ +A ++G + +
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRD 725
Query: 144 KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKR--FS 201
P+ + A LD++GI+ G V D+++G+T E E E R F
Sbjct: 726 IPH------LSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 779
Query: 202 K-----RDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV--------RIPQIGDKF 248
+ +D S + E GIV + D K VR V R Q+GDK
Sbjct: 780 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 839
Query: 249 ASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVN 284
A+RHG KG E + + D TP + +N
Sbjct: 840 ANRHGNKGVVAKILPVE---DMPHLPDGTPVDVILN 872
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 75.9 bits (185), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 56/89 (62%)
Query: 301 GNEVMFNGHTGRKINAQVFLGPTYYQRLKHMVDDKIHSRARGPVQILVRQPMEGRARDGG 360
G V+++G TG + +G + +L HMV+DK+H+R+ GP ++ +QP+ G+A+ GG
Sbjct: 969 GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGG 1028
Query: 361 LRFGEMERDCQISHGAAQFLRERLFEVSD 389
RFGEME ++GAA L+E L SD
Sbjct: 1029 QRFGEMEVWALEAYGAAHTLQEMLTIKSD 1057
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 59/216 (27%), Positives = 97/216 (44%), Gaps = 25/216 (11%)
Query: 85 LPAGINSIVAILCYTGYNQEDSVILNASAVERGYFRSVFFRSYK-DAESKRIGDQEEQFE 143
L G N +VAI+ + GYN ED+++++ ++R ++ S+ Y+ +A ++G + +
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRD 724
Query: 144 KPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDELEGTTKR--FS 201
P+ + A LD++GI+ G V D+++G+T E E E R F
Sbjct: 725 IPH------LSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 778
Query: 202 K-----RDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSV--------RIPQIGDKF 248
+ +D S + E GIV + D K VR V R Q+GDK
Sbjct: 779 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 838
Query: 249 ASRHGQKGTCGIQYRQEVSSNKGEIGDATPFNDAVN 284
A+RHG KG E + + D TP + +N
Sbjct: 839 ANRHGNKGVVAKILPVE---DMPHLPDGTPVDVILN 871
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 32/56 (57%)
Query: 393 IHVCNFCGLIAIANMRNNTFECKGCKNKTQISQVRLPYAAKLLFQELMSMNIAPRL 448
+ VC CG IA+ + R C C + +IS+V + YA KLL EL +M I P+L
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKL 60
>pdb|2I9I|A Chain A, Crystal Structure Of Helicobacter Pylori Protein Hp0492
Length = 254
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 51 LCYTGYNQEDSVILNASAVERGYFRSMEYLRFRELPAGINSIVAILC-YTGYNQEDSV-- 107
+ + Y E + +++ AVE G F++M Y G+NS +I+ Y N+ED++
Sbjct: 144 VWFNFYEPESNRVVHDFAVEVGTFQAMTYTYKHNNSGGLNSSNSIIHEYLEKNKEDAIHK 203
Query: 108 ILN 110
ILN
Sbjct: 204 ILN 206
>pdb|3TBI|B Chain B, Crystal Structure Of T4 Gp33 Bound To E. Coli Rnap
Beta-Flap Domain
Length = 228
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 8/60 (13%)
Query: 134 RIGDQEEQFEKPNRQTCQGMRNAIYDKLDDDGIIAPGLRVSGDDVVIGKTITLPENEDEL 193
++G +E + PN + A KLD+ GI+ G V+G D+++GK P+ E +L
Sbjct: 15 KLGPEEITADIPN------VGEAALSKLDESGIVYIGAEVTGGDILVGKVT--PKGETQL 66
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.138 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,910,961
Number of Sequences: 62578
Number of extensions: 527391
Number of successful extensions: 1156
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1100
Number of HSP's gapped (non-prelim): 39
length of query: 451
length of database: 14,973,337
effective HSP length: 102
effective length of query: 349
effective length of database: 8,590,381
effective search space: 2998042969
effective search space used: 2998042969
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)